Diptera is one of the most ecologically significant and species-rich insect orders, but there are still unresolved phylogenetic relationships among its basal lineages, particularly within the infraorder Blephariceromorpha, due to limited molecular data. To address this gap, this study employs two parallel genomic approaches: mitochondrial genomes and nuclear genomic analysis, covering 64 families and over 100 species of Diptera and their outgroups, to elucidate these phylogenetic relationships. Our results strongly support the monophyly of each constituent family (Blephariceridae, Deuterophlebiidae, and Nymphomyiidae), yet they reject the monophyly of Blephariceromorpha. Crucially, we found that Deuterophlebiidae and Nymphomyiidae form a sister group representing the basal-most lineage of Diptera, whereas Blephariceridae is positioned within Psychodomorpha. This indicates that the similar larval habitats and morphological traits shared between Blephariceridae and the Nymphomyiidae + Deuterophlebiidae clade are the result of convergent evolution. By resolving long-standing debates on the relationships within Blephariceromorpha and the basal lineages of Diptera, this study provides new insights into the evolutionary history of Diptera, especially within the suborder Nematocera.
Keywords: Diptera; Nematocera; mitogenomes; nuclear orthologs; phylogenomics.